We investigate the formation of non-ground-state Bose-Einstein condensates within the mean-field description represented by the Gross-Pitaevskii equation (GPE). The goal is to form excited states of a condensate known as nonlinear topological modes, which are stationary solutions of the GPE. Nonlinear modes can be generated by modulating either the trapping potential or the atomic scattering length. We show that it is possible to coherently control the transitions to excited nonlinear modes by manipulating the relative phase of the modulations. In addition, we show that the use of both modulations can modify the speed of the transitions. In our analysis, we employ approximate analytical techniques, including a perturbative treatment, and numerical calculations for the GPE. Our study evidences that the coherent control of the GPE presents novel possibilities which are not accessible for the Schrödinger equation. *